Designing a Novel Multi-Epitope Vaccine against SARS-CoV-2; Implication for Viral Binds and Fusion Inhibition through Inducing Neutralizing Antibodies

  1. Seyed Amir Hossein Mohammadzadeh Ho Moghri
  2. Mojtaba Ranjbar
  3. Hadi Hassannia
  4. Fatemeh Khakdan

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Abstract

Recently the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pervasive threat to public health so it is an emergency to vaccine development. The SARS-CoV-2 spike (S) glycoprotein plays a vital role in binds and fusion to the angiotensin-converting enzyme 2 (ACE2). The multi-epitope peptide vaccines are capable of inducing the specific humoral or cellular immune responses. In this regard, the RBD and spike cleavage site is the most probable target for vaccine development to inducing binds and fusion inhibitors neutralizing antibodies. In the present study, several immunoinformatics tools are used for analyzing the spike (S) glycoprotein sequence including the prediction of the potential linear B-cell epitopes, B-cell multi-epitope design, secondary and tertiary structures, physicochemical properties, solubility, antigenicity, and allergenicity for the promising vaccine candidate against SARS-CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2021.06.16.448772: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Recombinant DNA
    SentencesResources
    Finally, the optimized sequence (with added restriction sites) was inserted into the pET-28a(+) vector using the SnapGene restriction and insertion cloning module to ensure vaccine expression.
    pET-28a(+)
    suggested: RRID:Addgene_108949)
    Software and Algorithms
    SentencesResources
    2.4. Physiochemical properties, solubility, antigenicity and allergenicity prediction: Various physicochemical features of the RBD, including theoretical pI, instability index, aliphatic index, estimated half-life in the mammalian reticulocytes in vitro, extinction coefficient, grand average of hydropathicity (GRAVY), and molecular weight, were determined using the online web server ProtParam (http://web.expasy.org/protparam/) (17).
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    The peptide antigenicity characteristics were analyzed via VaxiJen v2.0 as an online antigen prediction server (http://www.ddgpharmfac.net/vaxijen/).
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    Secondary structure prediction: The secondary structure of the final peptide with position-specific iterated BLAST (PSI-blast) was predicted based on secondary structure PREDiction (PSIPRED) (http://bioinf.cs.ucl.ac.uk/psipred/) (21).
    http://bioinf.cs.ucl.ac.uk/psipred/
    suggested: (PSIPRED, RRID:SCR_010246)
    Tertiary structure prediction and validation: The three-dimensional (3D) structure of the spike (S) glycoprotein was downloaded from the Iterative Threading ASSEmbly Refinement (I-TASSER) server (https://zhanglab.ccmb.med.umich.edu/I-TASSER/).
    I-TASSER
    suggested: (I-TASSER, RRID:SCR_014627)
    Next, visualization and analyses were performed by building a 3D model in a PDB format using PyMOL (24).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 8 and 7. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    Results from rtransparent:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.06.16.448772 on bioRxiv